Do you have the latest updates installed. There were some issues with
the original release of the code that normalises to MNI space. Other
than that, I can't figure out what the cause of the problem could be.
Best regards,
-John
On Mon, 2009-09-28 at 17:44 +0200, Haakon Engen wrote:
> Dear Donald,
>
> That was my immediate thought as well. However, I've coregistered the
> T1 image to the mean functional image (output from the Realign:Unwarp
> module) for every subject. I have verified that the alignment between
> the T1 and functional images is within acceptable parameters for the
> standard Segment+ normalise procedure for all subjects, having already
> performed 1st and 2nd level analyses that I am hoping to compare with
> the DARTEL normalised data.
>
> Comparing the original T1, the Template, the flow field and the mean
> functional image yields the following for the two subjects (out of 39) I
> have used to test DARTEL as of yet.
>
> It seems like the normalisation procedure flips the EPI's for some, to
> me, obscure reason.
>
> Would skull stripping the images help in any way?
>
> Best wishes,
> h.
>
>
>
> On 28.09.2009 16:31, MCLAREN, Donald wrote:
> > Looks like your EPI images are aligned to the T1 images in native space
> > (orientation is different). Use check reg to see if the native space EPI
> > is aligned to the native space. If not, then you will need to align them
> > first and make sure the orientations are the same.
> >
> > On Mon, Sep 28, 2009 at 4:49 AM, Haakon Engen
> > <[log in to unmask] <mailto:[log in to unmask]>>
> > wrote:
> >
> > Dear SPM'ers,
> >
> > I'm running into some weirdness using DARTEL to normalise my
> > functional images. I have followed the recommended processing
> > pipeline in the manual, using the "New Segment" module to create
> > preimported rc*.img files that I've fed into the "Create templates"
> > module.
> >
> > After normalising the data the results don't look too good, as you
> > can see from the attached images. The functional images are severely
> > distorted, while the flow fields and template looks fine (albeit
> > from my limited understand of what fine DARTEL output is). Can
> > anyone help me figure out where I've messed up?
> >
> > Please let me know if you need any more information.
> >
> > Best wishes,
> > h.
> >
> >
> >
> >
> > --
> > Best Regards, Donald McLaren
> > =====================
> > Support the Alzheimer's Association Memory Walk 2009 ~~~
> > Join the Wisconsin Alzheimer's Disease Research Center team or make a
> > donation.
> > http://madison.kintera.org/2009/donaldmclaren
> >
> >
> > =================
> > D.G. McLaren
> > University of Wisconsin - Madison
> > Neuroscience Training Program
> > Office: (608) 265-9672
> > Lab: (608) 256-1901 ext 12914
> > =====================
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--
John Ashburner <[log in to unmask]>
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